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Summary  Interspecific genomic variation can provide a genetic basis for local adaptation and domestication. A series of studies have presented its role of interspecific haplotypes and introgressions in adaptive traits, but few studies have addressed their role in improving agronomic character. Two allotetraploid  Gossypium  species,  Gossypium barbadense  ( Gb ) and  G. hirsutum  ( Gh ) originating from the Americas, are cultivated independently. Here, through sequencing and the comparison of one GWAS panel in 229 Gb accessions and two GWAS panels in 491  Gh  accessions, we found that most associated loci or functional haplotypes for agronomic traits were highly divergent, representing the strong divergent improvement between  Gb  and  Gh . Using a comprehensive interspecific haplotype map, we revealed that six interspecific introgressions from  Gh  to  Gb  were significantly associated with the phenotypic performance of  Gb , which could explain 5%–40% of phenotypic variation in yield and fibre qualities. In addition, three introgressions overlapped with six associated loci in  Gb , indicating that these introgression regions were under further selection and stabilized during improvement. A single interspecific introgression often possessed yield‐increasing potential but decreased fibre qualities, or the opposite, making it difficult to simultaneously improve yield and fibre qualities. Our study not only has proved the importance of interspecific functional haplotypes or introgressions in the divergent improvement of  Gb  and  Gh , but also supports their potential value in further human‐mediated hybridization or precision breeding.

Divergent improvement of two cultivated allotetraploid cotton species